Protein functional features extracted from primary sequences: A focus on disordered sequences.

In this thesis we implement an ensemble of sequence analysis strategies aimed at identifying functional and structural protein features. The first part of this work was dedicated to two case studies of specific proteins analyzed to provide candidate func

Structural basis for the broad specificity of a new family of amino-acid racemases

Broad-spectrum amino-acid racemases (Bsrs) enable bacteria to generate noncanonical d-amino acids, the roles of which in microbial physiology, including the modulation of cell-wall structure and the dissolution of biofilms, are just beginning to be appreciated. Here, extensive crystallographic, mutational, biochemical and bioinformatic studies were used to define the molecular features of the racemase BsrV that enable this enzyme to accommodate more diverse substrates than the related PLP-dependent alanine racemases. Conserved residues were identified that distinguish BsrV and a newly defined family of broad-spectrum racemases from alanine racemases, and these residues were found to be key mediators of the multispecificity of BrsV. Finally, the structural analysis of an additional Bsr that was identified in the bioinformatic analysis confirmed that the distinguishing features of BrsV are conserved among Bsr family membersResearch in the Cava laboratory is supported by the MINECO, Spain (RYC-2010-06241), Universidad Autonoma de Madrid (UAM-38) and by the Knut and Alice Wallenberg Foundation (KAW). Additionally, this work was supported by the BFU2011-25326 MEC grant (JAH), by the S2010/BMD-2457 grant from CAM (JAH) and by HHMI (MKW

Structural Disorder Provides Increased Adaptability for Vesicle Trafficking Pathways

Vesicle trafficking systems play essential roles in the communication between the organelles of eukaryotic cells and also between cells and their environment. Endocytosis and the late secretory route are mediated by clathrin-coated vesicles, while the COat Protein I and II (COPI and COPII) routes stand for the bidirectional traffic between the ER and the Golgi apparatus. Despite similar fundamental organizations, the molecular machinery, functions, and evolutionary characteristics of the three systems are very different. In this work, we compiled the basic functional protein groups of the three main routes for human and yeast and analyzed them from the structural disorder perspective. We found similar overall disorder content in yeast and human proteins, confirming the well-conserved nature of these systems. Most functional groups contain highly disordered proteins, supporting the general importance of structural disorder in these routes, although some of them seem to heavily rely on disorder, while others do not. Interestingly, the clathrin system is significantly more disordered (,23%) than the other two, COPI (,9%) and COPII (,8%). We show that this structural phenomenon enhances the inherent plasticity and increased evolutionary adaptability of the clathrin system, which distinguishes it from the other two routes. Since multi-functionality (moonlighting) is indicative of both plasticity and adaptability, we studied its prevalence in vesicle trafficking proteins and correlated it with structural disorder. Clathrin adaptors have the highest capability for moonlighting while also comprising the most highly disordered members. The ability to acquire tissue specific functions was also used to approach adaptability: clathrin route genes have the most tissue specific exons encoding for protein segments enriched in structural disorder and interaction sites. Overall, our results confirm the general importance of structural disorder in vesicle trafficking and suggest major roles for this structural property in shaping the differences of evolutionary adaptability in the three routes

Comparison of systems in budding-associated functional groups of proteins.

<p>Comparison of disorder contents (%) predicted by the IUPred method between proteins involved in the three main vesicle trafficking systems for human (A) and yeast (B). Only data on budding and fission related proteins are presented here, since those could be reliably grouped according to the three main systems. Corresponding data are shown in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003144#pcbi-1003144-t001" target="_blank">Table 1</a>. The bottom and top border of the boxes represent 25% and 75% of the data respectively, while the bold line in the middle stands for the median (50%). The whiskers stand for the minimum and the maximum of the data, while the mean is depicted by a small red star.</p

Etude de la Pénalisation GraphNet en Analyse de Données Multi-blocs

International audienceL'intégration de données multiblocs est maintenant incontournable pour analyser des données complexes allant, par exemple, des données multi-omiques, aux données d'imagerie génétique. Par ailleurs, les bases de données biologiques de référence contiennent maintenant une information très riche qu'il convient d'intégrer dans de telles analyses.Nous proposons d'explorer la méthode netSGCCA qui permet l'intégration de réseaux dans le cadre de l'Analyse des Corrélations Canonique Généralisée pénalisée à l'aide d'une pénalité GraphNet. Plus particulièrement, nous souhaitons mettre en lumière un des désavantages de cette pénalité, qui est d'introduire des composantes ``haute-fréquence''.L'exemple que nous étudions est issu d'une étude clinique sur la Spondylarthrite ankylosante et comprend trois blocs : deux blocs de données d'expression, et un bloc de données cliniques. Le réseau de référence que nous utilisons est extrait de la base de données STRING-DB. Nous montrons sur cet exemple un moyen de ne conserver que les éléments ``basse fréquence'' induits par l'introduction de la pénalité GraphNet

Data on proteins with at least 5 off-pathway interactions from the three main routes.

<p>Same abbreviations used as in case of <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003144#pcbi-1003144-t001" target="_blank">Table 1</a>. CLTR stands for the clathrin route. Num. stands for number in the headers. Proteins are ordered according to the number of their off-pathway interaction partners.</p

Etude de la Pénalisation GraphNet en Analyse de Données Multi-blocs

International audienceL'intégration de données multiblocs est maintenant incontournable pour analyser des données complexes allant, par exemple, des données multi-omiques, aux données d'imagerie génétique. Par ailleurs, les bases de données biologiques de référence contiennent maintenant une information très riche qu'il convient d'intégrer dans de telles analyses.Nous proposons d'explorer la méthode netSGCCA qui permet l'intégration de réseaux dans le cadre de l'Analyse des Corrélations Canonique Généralisée pénalisée à l'aide d'une pénalité GraphNet. Plus particulièrement, nous souhaitons mettre en lumière un des désavantages de cette pénalité, qui est d'introduire des composantes ``haute-fréquence''.L'exemple que nous étudions est issu d'une étude clinique sur la Spondylarthrite ankylosante et comprend trois blocs : deux blocs de données d'expression, et un bloc de données cliniques. Le réseau de référence que nous utilisons est extrait de la base de données STRING-DB. Nous montrons sur cet exemple un moyen de ne conserver que les éléments ``basse fréquence'' induits par l'introduction de la pénalité GraphNet

Protein intrinsic disorder in plants

To some extent contradicting the classical paradigm of the relationship between protein 3D structure and function, now it is clear that large portions of the proteomes, especially in higher organisms, lack a fixed structure and still perform very important functions. Proteins completely or partially unstructured in their native (functional) form are involved in key cellular processes underlain by complex networks of protein interactions. The intrinsic conformational flexibility of these disordered proteins allows them to bind multiple partners in transient interactions of high specificity and low affinity. In concordance, in plants this type of proteins has been found in processes requiring these complex and versatile interaction networks. These include transcription factor networks, where disordered proteins act as integrators of different signals or link different transcription factor subnetworks due to their ability to interact (in many cases simultaneously) with different partners. Similarly, they also serve as signal integrators in signaling cascades, such as those related to response to external stimuli. Disordered proteins have also been found in plants in many stress-response processes, acting as protein chaperones or protecting other cellular components and structures. In plants, it is especially important to have complex and versatile networks able to quickly and efficiently respond to changing environmental conditions since these organisms cannot escape and have no other choice than adapting to them. Consequently, protein disorder can play an especially important role in plants, providing them with a fast mechanism to obtain complex, interconnected and versatile molecular networks.Peer reviewedPeer Reviewe

Interactions between pairs of clathrin-associated adaptor proteins.

<p>Complexes formed between clathrin-associated adaptor proteins are presented, in which one partner interacts with a region predicted to be structurally disordered in the unbound form. On the first three panels, the α2 subunit of mouse Ap-2 is the folded partner interacting with (A) rat epsin-1 (PDB 1KY6), (B) mouse intersectin-1 (PDB 3HS8); and (C) mouse EPS15 (Epidermal growth factor receptor substrate 15, PDB: 1KYF). In panel D, a relatively long disordered segment of human stonin-2 interacts with one folded EF-hand domain of human EPS15 (PDB: 2JXC). In each panel, the structure of the complex is depicted on the left and a domain map for each partner is depicted on the right. The top domain map represents the partner that is binding through the structurally disordered region. In panels A to C, the disordered peptides are represented with sticks (purple) while the folded partner is shown in surface representation (white). In panel D, the long disordered segment of human stonin-2 is shown in cartoon representation. For each protein, the domain maps indicate the names and locations of the known Pfam domains (predicted by the PfamScan method), and are shown in gray segments. Regions predicted to be disordered by IUPred are marked in purple segments; regions present in the PDB structure are marked by stars.</p